comparison vsnp_build_tables.xml @ 1:b60858c3eb91 draft

Uploaded

0:38a38babcb31

    #set input_json_dir = 'input_json_dir'
    mkdir $input_json_dir &&
    #for $i in $input_type_cond.input_avg_mq_json_collection:
        #set file_name = $i.file_name
        #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
        ln -s $file_name $input_json_avg_mq_dir/$identifier &&
    #end for
    #for $i in $input_type_cond.input_snps_json_collection:
        #set file_name = $i.file_name
        #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
        ln -s $file_name $input_json_dir/$identifier &&
    #end for
    #for $i in $input_type_cond.input_newick_collection:
        #set file_name = $i.file_name
        #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
        ln -s $file_name $input_newick_dir/$identifier &&
    #end for
#end if
python '$__tool_directory__/vsnp_build_tables.py'
--processes $processes
#if $input_type == "single":
    --input_avg_mq_json '$input_avg_mq_json'
    --input_snps_json '$input_snps_json'
    --input_newick '$input_newick'
#end if:

                    </when>
                </conditional>
            </when>
            <when value="no"/>
        </conditional>
        <param name="processes" type="integer" min="1" max="20" value="8" label="Number of processes for job splitting"/>
    </inputs>
    <outputs>
        <collection name="excel" type="list">
            <discover_datasets pattern="__name__" directory="output_excel_dir" format="xlsx" />
        </collection>

                    <element name="Mbovis-01D6_snps.json" value="Mbovis-01D6_snps.json" dbkey="89"/>
                </collection>
            </param>
            <param name="input_newick_collection">
                <collection type="list">
                    <element name="Mbovis-01_snps.json" value="Mbovis-01_snps.json" dbkey="89"/>
                    <element name="Mbovis-01D_snps.fasta" value="Mbovis-01D_snps.fasta" dbkey="89"/>
                    <element name="Mbovis-01D6_snps.fasta" value="Mbovis-01D6_snps.fasta" dbkey="89"/>
                </collection>
            </param>
            <param name="input_avg_mq_json_collection">
                <collection type="list">
                    <element name="Mbovis-01_snps.json" value="Mbovis-01_avg_mq.json" dbkey="89"/>

**Required Options**

 * **Choose the category for the files to be analyzed** -  select "Single files" or "Collections of files", then select the appropriate history items (single SNPs json, average MQ json and newick files, or collections of each) based on the selected option.
 * **Use Genbank file** - Select "yes" to annotate the tables using the information in the Genbank file.  Locally cached files, if available, provide the most widely used annotations, but more custom Genbank files can be chosen from the current history.
 * **Number of processes for job splitting** - Select the number of processes for splitting the job to shorten execution time.
    </help>
    <citations>
        <citation type="bibtex">
            @misc{None,
            journal = {None},

1:b60858c3eb91

    #set input_json_dir = 'input_json_dir'
    mkdir $input_json_dir &&
    #for $i in $input_type_cond.input_avg_mq_json_collection:
        #set file_name = $i.file_name
        #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
        ln -s '$file_name' '$input_json_avg_mq_dir/$identifier' &&
    #end for
    #for $i in $input_type_cond.input_snps_json_collection:
        #set file_name = $i.file_name
        #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
        ln -s '$file_name' '$input_json_dir/$identifier' &&
    #end for
    #for $i in $input_type_cond.input_newick_collection:
        #set file_name = $i.file_name
        #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
        ln -s '$file_name' '$input_newick_dir/$identifier' &&
    #end for
#end if
python '$__tool_directory__/vsnp_build_tables.py'
--processes \${GALAXY_SLOTS:-4}
#if $input_type == "single":
    --input_avg_mq_json '$input_avg_mq_json'
    --input_snps_json '$input_snps_json'
    --input_newick '$input_newick'
#end if:

                    </when>
                </conditional>
            </when>
            <when value="no"/>
        </conditional>
    </inputs>
    <outputs>
        <collection name="excel" type="list">
            <discover_datasets pattern="__name__" directory="output_excel_dir" format="xlsx" />
        </collection>

                    <element name="Mbovis-01D6_snps.json" value="Mbovis-01D6_snps.json" dbkey="89"/>
                </collection>
            </param>
            <param name="input_newick_collection">
                <collection type="list">
                    <element name="Mbovis-01_snps.newick" value="Mbovis-01_snps.newick" dbkey="89"/>
                    <element name="Mbovis-01D_snps.newick" value="Mbovis-01D_snps.newick" dbkey="89"/>
                    <element name="Mbovis-01D6_snps.newick" value="Mbovis-01D6_snps.newick" dbkey="89"/>
                </collection>
            </param>
            <param name="input_avg_mq_json_collection">
                <collection type="list">
                    <element name="Mbovis-01_snps.json" value="Mbovis-01_avg_mq.json" dbkey="89"/>

**Required Options**

 * **Choose the category for the files to be analyzed** -  select "Single files" or "Collections of files", then select the appropriate history items (single SNPs json, average MQ json and newick files, or collections of each) based on the selected option.
 * **Use Genbank file** - Select "yes" to annotate the tables using the information in the Genbank file.  Locally cached files, if available, provide the most widely used annotations, but more custom Genbank files can be chosen from the current history.
    </help>
    <citations>
        <citation type="bibtex">
            @misc{None,
            journal = {None},